Story #9044

[Crunch2] [Workbench] Browse and show tools using the GA4GH tool registry API

Added by Brett Smith over 5 years ago. Updated over 1 year ago.

Status:
New
Priority:
Normal
Assigned To:
Radhika Chippada
Category:
Workbench
Target version:
-
Start date:
Due date:
% Done:

0%

Estimated time:
Story points:
-

Description

This first version will just allow users to browse/select public workflows that have been registered at dockstore.org.

The API endpoint should be configurable, though, so that when Arvados supports the tool registry API itself (#9042) users will be able to select tools that are registered in Arvados.


Related issues

Related to Arvados - Story #9043: [Crunch2] [Workbench] Render CWL input selection formsResolved07/26/2016

History

#1 Updated by Tom Clegg over 5 years ago

  • Description updated (diff)
  • Category set to Workbench

#2 Updated by Tom Clegg over 5 years ago

  • Description updated (diff)

#3 Updated by Brett Smith over 5 years ago

  • Target version set to 2016-07-20 sprint

#4 Updated by Brett Smith over 5 years ago

  • Target version deleted (2016-07-20 sprint)

#5 Updated by Brett Smith over 5 years ago

  • Assigned To set to Radhika Chippada

Radhika's for grooming.

#6 Updated by Brett Smith over 5 years ago

  • Subject changed from [Crunch2] [Workbench] Browse and show tools using the tool registry API to [Crunch2] [Workbench] Browse and show tools using the GA4GH tool registry API

#7 Updated by Tom Morris about 5 years ago

  • Target version set to Arvados Future Sprints

#9 Updated by Radhika Chippada about 5 years ago

Implementation:

  • Add a “Run a tool” button in the panel header next to “Run a pipeline” in dashboard.
  • Add a config parameter to workbench to configure the tool registry end-point
  • When this button is pressed, present a “Choose a tool to run” modal similar to “Choose a pipeline to run” to the user
    • Get the tool json from the configured end point (do we want to cache this and pull at regular intervals or for each click?)
    • Present each version of each tool from the json as a separate link in the popup
      pcawg-merge-annotate - master
      pcawg-merge-annotate - 1.0.0
      …
      
    • When a link from the popup is clicked on, show the tool detail in preview pane on the right
    • When OK button is selected, create a CR with the selection as mount(s) and take the user to the CR page
    • The CR created for the selected tool version will have:
      • Name = tool - version (ex: pcawg-merge-annotate - master)
      • use mount kind json to store the selection
      • store the entire selected tool record including all version as mount point “/var/lib/cwl/tool”
      • store the selected tool version as mount “/var/lib/cwl/tool_version”

Out of scope for this story:

  • Support for json mount kind
  • Presenting appropriate input selection options based on the selected tool description
  • Running the selected tool

#10 Updated by Tom Morris about 5 years ago

  • Target version deleted (Arvados Future Sprints)

#11 Updated by Tom Morris over 3 years ago

  • Release deleted (11)

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